Zhang, You could perform the steps you show in 1., where you sample your ROI directly to the subjects surface, rather than going through the fsaverage subject. Ultimately, you would (or should) end-up with the same result as that from following the steps in the wiki page (going through fsaverage). The difference is that you only need to do the sampling of the ROI to fsaverage only once, whereas with what you want to do, you do it for every subject. Not a big deal if you dont have that many subjects. btw, fsaverage is in talairach space, so its not distorting things much by performing that registration (the .dat file from fslregister has very small values).
I'm not sure about the useful of performing 2., where you sample the thickness data to the volume. This is not usually done (I dont think). You will have a volume with voxel values equal to the thickness of the cortex around that voxel, but there is no hard meaning of that value for that voxel. Typically mri_surf2vol is used to sample parcellation labels into volume space. I'm not sure why you are getting dimension mismatch errors. Use mri_info on the files in question to get the dimensions. Note this part of the wiki instructions in the last two steps: cd $SUBJECTS_DIR/subjid/surf noting that 'subjid' is the name of your subject. If you remain in the $SUBJECTS_DIR/fsaverage/surf directory from the previous steps, you will get the mismatch error (which i just discovered myself). Nick On Fri, 2008-12-05 at 15:06 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote: > Hi Nick, > Thank you so much for your help! > Recently, I tested it strictly following your instruction. However, I > met a problem in the last step "mri_segstats ". They gave me the error > information: "ERROR: dimension mismatch between input volume and seg". > I checked the old mails in the list. Some one talked about dimension > mismatch but not related to my issue. Could you please do me a favor and > give some suggestion for the reason? > > There are another two issues: > 1. I noted you transfer ROI5.nii to fsaverage space. Because my ROI5.nii > have been in the Talairach space, can I transfer it to subjects's space > directly? > For example: > cd $SUBJECTS_DIR/subjid/surf > Fslregister --s subjid --mov /path/to/TT_avg152T1.nii --reg > TT_avg152T1_to_subjid.dat > Mri_vol2surf --mov /path/to/ROI5.nii --reg TT_avg152T1_to_subjid.dat > --projdist 0 1 0.1 --interp nearest --hemi lh --out lh.ROI5.mgh > Mri_segstats --seg lh.ROI5.mgh --in lh.thickness --sum segstats-ROI5.txt > > Is it OK? What is the benefit for using fsaverage data? > BTW, I got the same dimension mismatch error information in the last > step. > > 2. Can we transfer all data into the volume space. i.e., > Mri_surf2vol --surfval lh.thickness --hemi lh --fillribbon --template > orig.mgz --volregidentity subjid --outvol lh.ribbon.nii > Mri_convert lh.ribbon.nii --apply_transform > transforms/talairach.auto.xfm -o lh-talairach.ribbon.nii > > I tried it and no error information appear. However, I don't know it is > correct or not. > > Thanks, again! > > Xiaochu Zhang PhD > > Visiting Research Fellow > > Neuroimaging Research Branch > > National Institute on Drug Abuse - IRP > > Biomedical Research Center > > 251 Bayview Blvd. > > Suite 200 (NIDA) > > Baltimore MD > > 21224 > > Tel: 443-740-2619 > > > -----Original Message----- > From: Nick Schmansky [mailto:[EMAIL PROTECTED] > Sent: Friday, November 21, 2008 5:15 PM > To: Zhang, Xiaochu (NIH/NIDA) [F] > Cc: Freesurfer Mailing List; Allison Stevens > Subject: RE: [Freesurfer] RE: for cortical thickness > > Zhang, > > The web page describing the steps to extract cortical thickness data for > your volume-space defined ROI is found here: > > https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness > > Nick > > > On Mon, 2008-11-17 at 14:02 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote: > > Thank you so much for your response, Nick! > > I uploaded "ROI5.nii" (i.e., abc.nii) just now. This ROI has been in > > Talarich space. > > Actually, it is from my group functional data. So I did not have > > corresponding T1-data. > > > > BTW: when can I read the web page describing the steps taken to get > > cortical thickness from an ROI defined by a volume mask? I hope I can > > read it ASAP. If it is possible, could you please do me a favor and > > send the draft to me? > > Thanks, again! > > > > > > Xiaochu Zhang PhD > > > > Visiting Research Fellow > > > > Neuroimaging Research Branch > > > > National Institute on Drug Abuse - IRP > > > > Biomedical Research Center > > > > 251 Bayview Blvd. > > > > Suite 200 (NIDA) > > > > Baltimore MD > > > > 21224 > > > > Tel: 443-740-2619 > > > > > > -----Original Message----- > > From: Nick Schmansky [mailto:[EMAIL PROTECTED] > > Sent: Monday, November 17, 2008 12:59 PM > > To: Zhang, Xiaochu (NIH/NIDA) [F] > > Cc: Freesurfer Mailing List > > Subject: Re: [Freesurfer] RE: for cortical thickness > > > > Xiaochu, > > > > I'm putting together a web page describing the steps taken to get > > cortical thickness from an ROI defined by a volume mask. Can you send > > > me these two files so that I can make sure the steps work correctly? > > > > 1) the ROI mask file (what you are calling 'abc.nii') > > 2) the T1-weighted anatomical volume of the subject from which abc.nii > > > was created. i need this file to register to a template volume. > > > > You can post those files (available only to me) by uploading to our > > file > > drop: > > > > https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > Nick > > > > > > On Sat, 2008-11-15 at 00:48 -0500, Zhang, Xiaochu (NIH/NIDA) [F] > wrote: > > > Hi, FreeSurfer export, > > > > > > Thank you very much for response! > > > Now, under some export's help, I used to the mri_surf2vol to > > > transfer > > cortex thickness into nifti. > > > The below line is what I used. > > > mri_surf2vol --surfval ../surf/lh.thickness --hemi lh --fillribbon > > > --template orig.mgz --volregidentity ${subid} --outvol lh.ribbon.nii > > > > > > I checked the result and found the voxel outside the gray matter is > > always zero and in the gray matter is about 0-3. Could you please do > > me a favor and tell me whether these data is cortex thickness or not? > > > If they are cortex thickness, why are they always different. In my > > mind, it should be same in one direction because we calculate the > > distance between the white matter line and the gray matter line. > > > > > > Thanks a lot! > > > All the best, > > > Xiaochu > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
